Hello,
I am a user of Amber6. For the last few days i have
been trying to EM my protein of interest molecule,
which has two ZN atoms. Since Amber doesn`t have the
ZN ff parameters, so i generated the parameter file,
and also made a prep.in file. I also described the
restype of prep input file as protein, but still when
i run xleap, it doesn`t reconizes ZN. Each time it
gives the error message that ZN does not have a type,
and the parameters file are not saved.
My prep input file
HISTIDINE DELTAH
HIC INT 1
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 0.000
0.000 0.00000
2 DUMM DU M 1 0 -1 1.449 0.000
0.000 0.00000
3 DUMM DU M 2 1 0 1.522 111.100
0.000 0.00000
4 N N M 3 2 1 1.335 116.600
180.000 -0.41570
5 H H E 4 3 2 1.010 119.800
0.000 0.27190
6 CA CT M 4 3 2 1.449 121.900
180.000 0.01880
7 HA H1 E 6 4 3 1.090 109.500
300.000 0.08810
8 CB CT 3 6 4 3 1.525 111.100
60.000 -0.04620
9 HB2 HC E 8 6 4 1.090 109.500
300.000 0.04020
10 HB3 HC E 8 6 4 1.090 109.500
60.000 0.04020
11 CG CC S 8 6 4 1.510 115.000
180.000 -0.02660
12 ND1 NA B 11 8 6 1.390 122.000
180.000 -0.38110
13 HD1 H E 12 11 8 1.010 126.000
0.000 0.36490
14 CE1 CR B 12 11 8 1.320 108.000
180.000 0.20570
15 HE1 H5 E 14 12 11 1.090 120.000
180.000 0.13920
16 NE2 NB S 14 12 11 1.310 109.000
0.000 -0.57270
17 ZN1 ZN E 16 14 12 2.050 126.000
0.000 +2.00000
18 CD2 CV S 16 14 12 1.360 110.000
0.000 0.12920
18 HD2 H4 E 18 16 14 1.090 120.000
180.000 0.11470
19 C C M 6 4 3 1.522 111.100
180.000 0.59730
20 O O E 20 6 4 1.229 120.500
0.000 -0.56790
LOOP
CG CD2
IMPROPER
-M CA N H
CA +M C O
CG CE1 ND1 HD1
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
DONE
STOP
My leap.in file
frcmod = loadamberparams frcmod.pcy
loadAmberPrep hic.in
set HIC restype protein
plc = loadPdb 1cp6H.pdb
bond plc.223.SG plc.227.SG
bond plc.256.NE2 plc.292.ZN1
solvatebox plc WATBOX216 5. 1.
saveAmberParm plc 1cp6.top 1cp6.crd
My ff file for Zn
# modifications to force field for aminopeptidase
MASS
ZN 65.38
BOND
ZN-N 40.000 2.05000 J Am. Chem.Soc
vol113, No-22, 1991
ZN-OH 94.000 1.80000 do
ZN-OH2 40.000 2.05000 do
ANGLE
C-N-ZN 20.000 126.000 DO
H-O-ZN 100.000 126.000 DO
N-ZN-N 109.500 20.000 DO
N-ZN-O 109.500 20.000 DO
DIHE
X -ZN-N -X 1 0.000 0.000 3.000
X -ZN-O -X 1 0.000 0.000 3.000
NONBON
ZN 1.10 0.0125
I would be highly obliged if you can advice me on this
problem.
Thanking you in anticipation.
Amit
=====
Amit Kumar
Graduate Student
Biophysics Research Institute
Medical College of Wisconsin
Milwaukee.
Phone(home) 414-476-7834
Phone(office) 414-456-4590
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Received on Mon Sep 16 2002 - 09:25:05 PDT
